Hierarchical Partitioning

Summary

  • Ctenophorus fordi - spinifex and bare are significant.
  • Ctenotus atlas - spinifex and bare ground are significant.
  • Ctenotus schomburgkii - clay is significant.
  • Lerista distinguenda - spinifex is significant.
  • Lerista edwardsae - no single factor significant. Melaleuca then bare are the highest.
  • Menetia greyii - Bare ground significant.
  • Nephrurus stellatus - Bare ground is significant.
  • Pogona sp. - Melaleuca is significant.

Joint was not very high for any species.

Spinifex, bare ground, and leaf litter varied significantly (P < 0.05) between the five site treatments (Connected, Isolated, ParkDune, ParkSwale, Roadside).

When looking at Conn (Connected, Disconnected) and Setting (Park, Dune), Setting was significant for spinifex. Nothing else was significant at P<0.05.

Using LME

Reptiles

  • Cten ford - setting
  • Cten atla - setting
  • Cten scho - setting
  • Leri dist - setting
  • Mene grey - setting, dune, site:dune
  • Neph stel - dune
  • Pogo sp - NONE
  • NumSpec - setting, site:conn (log+1)
  • Sum - setting (log+1)

Vegetation

  • Spinifex - setting, setting:dune - significantly higher in park. Park swale > Park dunes. Farm dune > Farm swale (no spinifex in farm swales)
  • Melaleuca - setting:dune- farm dune > park dune, park swale > farm swale
  • Eucalyptus - site:setting - farm dunes < farm swales, park dunes > swale
  • Bare - dune - higher in dune
  • Leaf - dune, setting:dune, site:setting:dune
  • Other - site:setting, setting:dune, site:setting:dune
  • Clay - dune - higher in swale
  • Canopy - dune, site:setting - Hincks farm > Pinks farm, Pinks park > Hinks park
  • NumSpec -setting, site:conn, Hincks connected > Pinks connected, Pinks isolated > Hincks isolated
  • Sum - setting - more animals in park
  • which veg things are different between park and reserve?

Code

 # Test the five site treatments on continuous vegetation data
 for (name in c(attributes(env)$names)) {
   envvar <- epdata[[name]]
   print(name)
   a <- aov(envvar ~ TreatCode, data=epdata)
   print(summary(a))
 }

 # LME tests of species counts vs formal structure 
 # nb - is it meaningful to log+1 transform number of species? Either way, same parameters were significant.
 for (name in c(attributes(lotsacritters)$names,"NumSpec","Sum")) {
    species<-epdata[[name]]
    print(name)
    mod<-lme(log(1+species) ~ Site + Setting + Dune + Conn
        + Site:Setting + Site:Dune + Site:Conn
        + Setting:Dune + Setting:Dune:Site,
        random = ~1|Block,
        data=epdata,
        method="ML")
    print(anova(mod))
 }

 # LME tests of veg data vs formal structure
 for (name in c(attributes(env)$names, "NumSpec", "Sum")) {
  veg<-epdata[[name]]
  print(name)
  mod<-lme(veg ~ Site + Setting + Dune + Conn
    + Site:Setting + Site:Dune + Site:Conn
    + Setting:Dune + Setting:Dune:Site, 
    random = ~1|Block,
    data=epdata,
    method="ML")
    print(anova(mod))
 }

Ctenophorus fordi

$IJ
                     I            J       Total
Spinifex   0.282519609  0.053795696 0.336315305
Melaleuca  0.004119899  0.000889869 0.005009768
Eucalyptus 0.017213825  0.005975337 0.023189162
Bare       0.108952403  0.018625901 0.127578304
Leaf       0.055508647 -0.010063317 0.045445331
Other      0.031691511 -0.029826892 0.001864619
Clay       0.007497372  0.001082470 0.008579842
Canopy     0.029493098 -0.016444191 0.013048907


 $I.perc
                     I
 Spinifex   52.6110840 0.027 *
 Melaleuca   0.7672117 0.839
 Eucalyptus  3.2055758 0.485
 Bare       20.2892255 0.070 .
 Leaf       10.3368758 0.199
 Other       5.9016249 0.305
 Clay        1.3961681 0.739
 Canopy      5.4922342 0.384

Setting    24.5132084 0.013
Spinifex   35.5790558 0.029
Melaleuca   0.6008803 0.877
Eucalyptus  4.0676255 0.345
Bare       16.4034445 0.071
Leaf        8.6495974 0.221
Other       3.2757966 0.536
Clay        0.9567297 0.806
Canopy      5.9536618 0.331

Including condition and setting:

$IJ
                       I             J       Total
Setting     0.0789431157  0.1773859982 0.256329114
Condition   0.0294446182  0.1019102599 0.131354878
Spinifex    0.1163063281  0.2200089766 0.336315305
Melaleuca  -0.0004874122  0.0054971803 0.005009768
Eucalyptus  0.0082522630  0.0149368991 0.023189162
Bare        0.0449315548  0.0826467493 0.127578304
Leaf        0.0148009251  0.0306444055 0.045445331
Other       0.0024835818 -0.0006189629 0.001864619
Clay        0.0013572105  0.0072226311 0.008579842
Canopy      0.0344263895 -0.0213774821 0.013048907

$I.perc
                    I
Setting    23.8889597 0.002 **
Condition   8.9102298  0.164
Spinifex   35.1954336 0.025 *
Melaleuca  -0.1474957 1.000
Eucalyptus  2.4972156 0.523
Bare       13.5967284 0.100
Leaf        4.4789048 0.374
Other       0.7515562 0.913
Clay        0.4107052 0.910
Canopy     10.4177625 0.322

Ctenotus atlas

$IJ
                    I            J        Total
Spinifex   0.13468950  0.045250568 1.799401e-01
Melaleuca  0.05499363  0.021555405 7.654904e-02
Eucalyptus 0.05818458 -0.001471621 5.671296e-02
Bare       0.10872661  0.043340162 1.520668e-01
Leaf       0.01142134 -0.011330472 9.086391e-05
Other      0.03047367 -0.014637202 1.583647e-02
Clay       0.00592294 -0.001512726 4.410214e-03
Canopy     0.01291559  0.018413198 3.132879e-02

$I.perc
                   I
Spinifex   32.274264 0.028 *
Melaleuca  13.177561 0.200
Eucalyptus 13.942175 0.154
Bare       26.053044 0.068 .
Leaf        2.736778 0.716
Other       7.302094 0.396
Clay        1.419253 0.781
Canopy      3.094831 0.700
Setting    35.1161831 0.016
Spinifex   15.3046099 0.111
Melaleuca   9.4886690 0.195
Eucalyptus 14.1790256 0.116
Bare       17.4852104 0.084
Leaf        2.5040231 0.659
Other       3.1871242 0.573
Clay        0.5524115 0.931
Canopy      2.1827433 0.765

Including condition and setting:

$IJ
                       I            J        Total
Setting     0.0850725881  0.202765652 2.878382e-01
Condition   0.0810476061  0.209020368 2.900680e-01
Spinifex    0.0460075757  0.133932491 1.799401e-01
Melaleuca   0.0225981500  0.053950890 7.654904e-02
Eucalyptus  0.0385725802  0.018140381 5.671296e-02
Bare        0.0479264148  0.104140361 1.520668e-01
Leaf        0.0046114950 -0.004520631 9.086391e-05
Other       0.0064443959  0.009392075 1.583647e-02
Clay       -0.0003957471  0.004805961 4.410214e-03
Canopy      0.0136110270  0.017717763 3.132879e-02

$I.perc
                    I
Setting    24.6233146 0.012 *
Condition  23.4583283 0.019 *
Spinifex   13.3163812 0.094 .
Melaleuca   6.5407832 0.256
Eucalyptus 11.1644044 0.113
Bare       13.8717678 0.101
Leaf        1.3347459 0.733
Other       1.8652587 0.681
Clay       -0.1145446 0.998
Canopy      3.9395604 0.711

Ctenotus schomburgkii

                     I            J        Total
Spinifex   0.007693853 -0.001357805 0.0063360479
Melaleuca  0.014093235 -0.013730399 0.0003628356
Eucalyptus 0.055730411  0.048853066 0.1045834775
Bare       0.050082097  0.031982205 0.0820643018
Leaf       0.031562937  0.065062025 0.0966249615
Other      0.075530605 -0.037602979 0.0379276263
Clay       0.119076878  0.048023720 0.1671005979
Canopy     0.040694868  0.033658265 0.0743531326

$I.perc
                   I
Spinifex    1.950453 0.717
Melaleuca   3.572748 0.580
Eucalyptus 14.128105 0.133
Bare       12.696212 0.206
Leaf        8.001457 0.380
Other      19.147612 0.095 .
Clay       30.186940 0.060 .
Canopy     10.316474 0.264

Including setting:

Setting    35.720563  0.001
Spinifex    3.911020  0.428
Melaleuca   2.059892  0.591
Eucalyptus  8.027591  0.210
Bare        8.117147  0.266
Leaf        5.678909  0.395
Other       8.083982  0.217
Clay       19.005655  0.075
Canopy      9.395242  0.244

Including condition and setting:

                      I            J        Total
Setting    0.0804953198  0.118082361 0.1985776805
Condition  0.0373524086  0.064407967 0.1017603761
Spinifex   0.0113189307 -0.004982883 0.0063360479
Melaleuca  0.0008819496 -0.000519114 0.0003628356
Eucalyptus 0.0293474992  0.075235978 0.1045834775
Bare       0.0215999924  0.060464309 0.0820643018
Leaf       0.0241960724  0.072428889 0.0966249615
Other      0.0148067348  0.023120892 0.0379276263
Clay       0.0727332909  0.094367307 0.1671005979
Canopy     0.0568532257  0.017499907 0.0743531326

$I.perc
                    I
Setting    23.0259371 0.001 ***
Condition  10.6847729 0.115
Spinifex    3.2378154 0.396
Melaleuca   0.2522844 0.959
Eucalyptus  8.3949436 0.149
Bare        6.1787451 0.258
Leaf        6.9213619 0.226
Other       4.2355126 0.302
Clay       20.8055845 0.050 *
Canopy     16.2630424 0.184

Lerista.distinguenda

$IJ
                     I            J        Total
Spinifex   0.158548186  0.034402921 1.929511e-01
Melaleuca  0.008878447  0.012691453 2.156990e-02
Eucalyptus 0.006565441  0.014601900 2.116734e-02
Bare       0.008518065 -0.002356438 6.161628e-03
Leaf       0.010665160  0.001849853 1.251501e-02
Other      0.006058410 -0.005992105 6.630434e-05
Clay       0.016264492  0.032209067 4.847356e-02
Canopy     0.033279092  0.030382187 6.366128e-02

$I.perc
                   I
Spinifex   63.730972 0.023
Melaleuca   3.568833 0.671
Eucalyptus  2.639084 0.841
Bare        3.423972 0.738
Leaf        4.287031 0.727
Other       2.435274 0.898
Clay        6.537772 0.543
Canopy     13.377062 0.351
Setting    54.174420 0.002
Spinifex   21.487833  0.087
Melaleuca   1.949073  0.696
Eucalyptus  2.998589  0.645
Bare        1.889921  0.742
Leaf        3.313789 0.657
Other       3.073721 0.708
Clay        5.127236 0.450
Canopy      5.985417 0.446

With condition and setting:

$IJ
                     I            J        Total
Setting    0.096030967  0.204872402 3.009034e-01
Condition  0.106655834  0.222735269 3.293911e-01
Spinifex   0.050400390  0.142550717 1.929511e-01
Melaleuca  0.003562767  0.018007133 2.156990e-02
Eucalyptus 0.009263527  0.011903814 2.116734e-02
Bare       0.002295763  0.003865865 6.161628e-03
Leaf       0.001554563  0.010960449 1.251501e-02
Other      0.001606906 -0.001540602 6.630434e-05
Clay       0.010656184  0.037817375 4.847356e-02
Canopy     0.018915523  0.044745756 6.366128e-02

$I.perc
                    I
Setting    31.9100797 0.011 *
Condition  35.4406109 0.001 ***
Spinifex   16.7475190 0.073 .
Melaleuca   1.1838701 0.782
Eucalyptus  3.0781724 0.524
Bare        0.7628579 0.837
Leaf        0.5165650 0.940
Other       0.5339581 0.963
Clay        3.5409376 0.455
Canopy      6.2854292 0.539

Lerista edwardsae

$IJ
                     I            J        Total
Spinifex   0.068770068  0.018098802 0.0868688705
Melaleuca  0.103633078  0.049848858 0.1534819356
Eucalyptus 0.005292995 -0.002890250 0.0024027450
Bare       0.079393097 -0.038382266 0.0410108306
Leaf       0.031066343 -0.030907214 0.0001591293
Other      0.045608649  0.036542347 0.0821509953
Clay       0.025790353  0.007842244 0.0336325966
Canopy     0.014295718 -0.011515882 0.0027798368

$I.perc
                   I
Spinifex   18.395082 0.134
Melaleuca  27.720475 0.064 .
Eucalyptus  1.415806 0.854
Bare       21.236601 0.109
Leaf        8.309835 0.370
Other      12.199709 0.221
Clay        6.898577 0.385
Canopy      3.823915 0.624
Spinifex                              6.5606680 0.263
Melaleuca                            16.4097518 0.069
Eucalyptus                            0.8614492 0.893
Bare                                 11.3054938 0.133
Leaf                                  5.6088447 0.334
Other                                 9.7576900 0.151
Clay                                  2.9712002 0.528
Canopy                                3.8089638 0.446
epdata...Site....epdata...Setting... 42.7159385 0.018


Setting    19.497802 0.080
Spinifex    9.019138 0.226
Melaleuca  20.983543 0.074
Eucalyptus  1.030877 0.889
Bare       18.035756 0.086
Leaf        7.809179 0.310
Other      13.829650 0.141
Clay        7.172307 0.310
Canopy      2.621747 0.702

Including condition and setting:

$IJ
                     I            J        Total
Setting    0.029225864  0.044476819 0.0737026824
Condition  0.113828312  0.147666909 0.2614952208
Spinifex   0.022806085  0.064062785 0.0868688705
Melaleuca  0.047618731  0.105863205 0.1534819356
Eucalyptus 0.003514044 -0.001111299 0.0024027450
Bare       0.045952736 -0.004941906 0.0410108306
Leaf       0.009335224 -0.009176095 0.0001591293
Other      0.036534017  0.045616979 0.0821509953
Clay       0.013559729  0.020072868 0.0336325966
Canopy     0.009580873 -0.006801036 0.0027798368

$I.perc
                   I
Setting     8.804148 0.209
Condition  34.290220 0.003 ***
Spinifex    6.870221 0.193
Melaleuca  14.344909 0.077
Eucalyptus  1.058588 0.768
Bare       13.843036 0.104
Leaf        2.812191 0.506
Other      11.005693 0.091
Clay        4.084802 0.398
Canopy      2.886191 0.785

Menetia greyii


$IJ
                    I            J        Total
Spinifex   0.10580019 -0.021682476 8.411771e-02
Melaleuca  0.05184491  0.007643409 5.948832e-02
Eucalyptus 0.01162429 -0.009358820 2.265469e-03
Bare       0.14144477 -0.079599815 6.184495e-02
Leaf       0.03173728 -0.031726563 1.071934e-05
Other      0.01392941 -0.011531731 2.397680e-03
Clay       0.05242940  0.015877986 6.830738e-02
Canopy     0.01223926 -0.002058008 1.018125e-02

$I.perc
                   I
Spinifex   25.127731 0.067 .
Melaleuca  12.313258 0.197
Eucalyptus  2.760789 0.647
Bare       33.593382 0.032 *
Leaf        7.537661 0.363
Other       3.308260 0.672
Clay       12.452074 0.192
Canopy      2.906845 0.728
Setting                              11.482420 0.101
Aspect                                9.678386 0.162
epdata...Setting....epdata...Dune... 27.852460 0.065
Spinifex                             10.420934 0.147
Melaleuca                             7.788696 0.298
Eucalyptus                            2.000454 0.800
Bare                                 10.333203 0.201
Leaf                                  5.748670 0.421
Other                                 2.422753 0.799
Clay                                  9.524762 0.174
Canopy                                2.747264 0.665

Including condition, setting:dune:

                                              I            J        Total
Setting                              0.02483714  0.079930614 1.047678e-01
Aspect                               0.02462170  0.055591110 8.021281e-02
epdata...Setting....epdata...Dune... 0.06201528  0.196732414 2.587477e-01
Condition                            0.04307311  0.122458698 1.655318e-01
Spinifex                             0.02533964  0.058778074 8.411771e-02
Melaleuca                            0.01986015  0.039628174 5.948832e-02
Eucalyptus                           0.00837537 -0.006109900 2.265469e-03
Bare                                 0.02846058  0.033384377 6.184495e-02
Leaf                                 0.01369576 -0.013685042 1.071934e-05
Other                                0.00802862 -0.005630940 2.397680e-03
Clay                                 0.01921285  0.049094533 6.830738e-02
Canopy                               0.01269663 -0.002515378 1.018125e-02

$I.perc
                                             I
Setting                               8.558132 0.174
Aspect                                8.483898 0.227
Setting:Dune                     21.368604 0.102
Condition                            14.841701 0.040 *
Spinifex                              8.731278 0.238
Melaleuca                             6.843210 0.322
Eucalyptus                            2.885901 0.743
Bare                                  9.806660 0.192
Leaf                                  4.719148 0.519
Other                                 2.766421 0.715
Clay                                  6.620171 0.289
Canopy                                4.374876 0.509

Nephrurus stellatus

$IJ
                     I            J       Total
Spinifex   0.018561305  0.001120501 0.019681807
Melaleuca  0.022830083  0.002005971 0.024836054
Eucalyptus 0.036956313 -0.031714796 0.005241517
Bare       0.161381675 -0.029211398 0.132170277
Leaf       0.033803446  0.059333287 0.093136733
Other      0.008584501 -0.001055600 0.007528901
Clay       0.064951205  0.053060102 0.118011306
Canopy     0.051488981  0.027776005 0.079264986

$I.perc
                   I
Spinifex    4.657121 0.474
Melaleuca   5.728178 0.453
Eucalyptus  9.272517 0.275
Bare       40.491440 0.023 *
Leaf        8.481447 0.349
Other       2.153893 0.817
Clay       16.296570 0.142
Canopy     12.918833 0.189
Aspect     24.530918 0.063
Spinifex    5.533636 0.474
Melaleuca   5.625037 0.434
Eucalyptus  8.265105 0.344
Bare       25.580785 0.074
Leaf        6.580042 0.434
Other       2.149101 0.828
Clay       11.654051 0.206
Canopy     10.081325 0.288

Including condition, dune:

$IJ
                     I           J       Total
Aspect     0.072870167 0.145123008 0.217993175
Condition  0.043846845 0.038774870 0.082621714
Spinifex   0.006880230 0.012801577 0.019681807
Melaleuca  0.006692614 0.018143440 0.024836054
Eucalyptus 0.003802960 0.001438557 0.005241517
Bare       0.059243901 0.072926376 0.132170277
Leaf       0.021304115 0.071832618 0.093136733
Other      0.003329119 0.004199783 0.007528901
Clay       0.033615470 0.084395836 0.118011306
Canopy     0.031333695 0.047931291 0.079264986

$I.perc
                   I
Aspect     25.756537 0.017 *
Condition  15.498014 0.090
Spinifex    2.431872 0.593
Melaleuca   2.365557 0.622
Eucalyptus  1.344186 0.776
Bare       20.940225 0.059
Leaf        7.530108 0.265
Other       1.176703 0.823
Clay       11.881654 0.135
Canopy     11.075142 0.345


Pogona sp.

$IJ
                     I            J       Total
Spinifex   0.004499951  0.004198701 0.008698652
Melaleuca  0.196274074  0.030004011 0.226278085
Eucalyptus 0.036317153  0.015002119 0.051319272
Bare       0.007197359  0.005920677 0.013118036
Leaf       0.015019426  0.003040418 0.018059844
Other      0.019036686  0.020284764 0.039321450
Clay       0.034212471 -0.015982038 0.018230433
Canopy     0.007506271 -0.007026771 0.000479500

$I.perc
                   I
Spinifex    1.405956 0.863
Melaleuca  61.323500 0.016 *
Eucalyptus 11.346863 0.329
Bare        2.248729 0.748
Leaf        4.692641 0.635
Other       5.947786 0.557
Clay       10.689280 0.341
Canopy      2.345245 0.864
Spinifex    1.405956 0.860
Melaleuca  61.323500 0.009
Eucalyptus 11.346863 0.288
Bare        2.248729 0.769
Leaf        4.692641 0.619
Other       5.947786 0.552
Clay       10.689280 0.334
Canopy      2.345245 0.848

Including condition:

                   I
Condition   7.312277 0.399
Spinifex    2.463616 0.732
Melaleuca  59.182230 0.005 ***
Eucalyptus  8.481841 0.332
Bare        1.592537 0.819
Leaf        4.160797 0.641
Other       5.963511 0.499
Clay        9.300349  0.315
Canopy      1.542842 0.941

NumSpec

$IJ
                     I            J       Total
Spinifex   0.022292769  0.001184860 0.023477629
Melaleuca  0.005981831 -0.003412719 0.002569112
Eucalyptus 0.005982440 -0.002009065 0.003973374
Bare       0.084434851  0.044125017 0.128559868
Leaf       0.012477617 -0.011453804 0.001023814
Other      0.041026452  0.021223510 0.062249961
Clay       0.079129974 -0.062584982 0.016544991
Canopy     0.093819398 -0.013990933 0.079828465

$I.perc
                   I
Spinifex    6.458951 0.481
Melaleuca   1.733134 0.791
Eucalyptus  1.733310 0.842
Bare       24.463565 0.108
Leaf        3.615178 0.709
Other      11.886718 0.272
Clay       22.926566 0.112
Canopy     27.182578 0.072 .
epdata...Site....epdata...Conn... 23.5950103 0.166
Setting                           32.0841295 0.003
Spinifex                           2.7284507 0.444
Melaleuca                          1.2891081 0.611
Eucalyptus                         1.0208294 0.716
Bare                              13.6362620 0.063
Leaf                               0.4136983 0.886
Other                              5.7654162 0.236
Clay                               3.0478780 0.416
Canopy                            16.4192175 0.136

Including condition, setting, site:conn:

$IJ
                                           I             J       Total
Site:Conn                         0.07782809  0.1033055644 0.181133654
Setting                           0.08386831  0.1922594215 0.276127728
Condition                         0.09744256  0.1998319709 0.297274527
Spinifex                          0.01986955  0.0036080802 0.023477629
Melaleuca                         0.01494238 -0.0123732726 0.002569112
Eucalyptus                        0.01752548 -0.0135521088 0.003973374
Bare                              0.04621075  0.0823491225 0.128559868
Leaf                              0.01327935 -0.0122555341 0.001023814
Other                             0.02848004  0.0337699168 0.062249961
Clay                              0.01643272  0.0001122722 0.016544991
Canopy                            0.02230745  0.0575210137 0.079828465

$I.perc
                                          I
Site:Conn                         17.761400 0.092
Setting                           19.139858 0.006 **
Condition                         22.237681 0.002 **
Spinifex                           4.534494 0.305
Melaleuca                          3.410050 0.438
Eucalyptus                         3.999547 0.368
Bare                              10.545904 0.058
Leaf                               3.030523 0.480
Other                              6.499523 0.191
Clay                               3.750164 0.339
Canopy                             5.090856 0.280

Sum

$IJ
                     I            J        Total
Spinifex   0.020554995  0.005706324 0.0262613190
Melaleuca  0.005146626 -0.005016252 0.0001303742
Eucalyptus 0.008323711  0.005767381 0.0140910920
Bare       0.024068061  0.015561843 0.0396299037
Leaf       0.018385680  0.009908405 0.0282940853
Other      0.070021978  0.017306896 0.0873288740
Clay       0.009129871  0.010407720 0.0195375913
Canopy     0.068901978  0.061920175 0.1308221526

$I.perc
                   I
Spinifex    9.154558 0.464
Melaleuca   2.292148 0.822
Eucalyptus  3.707123 0.731
Bare       10.719169 0.432
Leaf        8.188413 0.585
Other      31.185620 0.120
Clay        4.066162 0.705
Canopy     30.686807 0.144
Setting    53.6825722 0.012
Spinifex    4.3199237 0.574
Melaleuca   0.9102594 0.896
Eucalyptus  1.7789326 0.833
Bare        5.2798853 0.483
Leaf        4.0610673 0.630
Other      12.3265543 0.260
Clay        1.7913453 0.786
Canopy     15.8494599 0.197

Including condition and setting:

$IJ
                     I            J        Total
Setting    0.082790194  0.184219843 0.2670100363
Condition  0.103363813  0.185953554 0.2893173669
Spinifex   0.008098196  0.018163123 0.0262613190
Melaleuca  0.002095943 -0.001965569 0.0001303742
Eucalyptus 0.006310573  0.007780519 0.0140910920
Bare       0.009794153  0.029835750 0.0396299037
Leaf       0.010328867  0.017965218 0.0282940853
Other      0.030083529  0.057245345 0.0873288740
Clay       0.002719269  0.016818322 0.0195375913
Canopy     0.044186903  0.086635250 0.1308221526

$I.perc
                    I
Setting    27.6177724 0.018 *
Condition  34.4808742 0.005 ***
Spinifex    2.7014567 0.586
Melaleuca   0.6991803 0.889
Eucalyptus  2.1051282 0.654
Bare        3.2672070 0.523
Leaf        3.4455808 0.499
Other      10.0354886 0.189
Clay        0.9071141 0.822
Canopy     14.7401977 0.247

RareSp

$IJ
                     I             J       Total
Spinifex   0.041990170 -0.0050859832 0.036904187
Melaleuca  0.022736797  0.0138569898 0.036593787
Eucalyptus 0.011464087 -0.0060269176 0.005437170
Bare       0.053109171  0.0089307065 0.062039877
Leaf       0.035077433 -0.0215004832 0.013576950
Other      0.060558287  0.0871025975 0.147660884
Clay       0.004586129 -0.0006186097 0.003967519
Canopy     0.076575567 -0.0057035333 0.070872033

$I.perc
                   I
Spinifex   13.717901 0.258
Melaleuca   7.427956 0.444
Eucalyptus  3.745239 0.639
Bare       17.350402 0.203
Leaf       11.459557 0.345
Other      19.783977 0.169
Clay        1.498257 0.832
Canopy     25.016712 0.113
epdata...Site....epdata...Conn... 47.1985947 0.050
Spinifex                           8.7879264 0.215
Melaleuca                          2.6218967 0.572
Eucalyptus                         1.2920455 0.810
Bare                              10.0691191 0.189
Leaf                               6.1883155 0.335
Other                              9.5730578 0.179
Clay                               0.9269207 0.865
Canopy                            13.3421235 0.097

Including condition and site:conn:

$IJ
                                            I            J       Total
Site:Conn                           0.131022488  0.164548353 0.295570841
Condition                         0.044971245  0.031116462 0.076087707
Spinifex                          0.030803975  0.006100212 0.036904187
Melaleuca                         0.012899747  0.023694040 0.036593787
Eucalyptus                        0.006443976 -0.001006807 0.005437170
Bare                              0.027196487  0.034843391 0.062039877
Leaf                              0.006359432  0.007217519 0.013576950
Other                             0.040996249  0.106664635 0.147660884
Clay                              0.001041845  0.002925673 0.003967519
Canopy                            0.054004761  0.016867272 0.070872033

$I.perc
                                           I
Site:Conn                           36.8309474 0.058
Condition                         12.6415975 0.092
Spinifex                           8.6591211 0.142
Melaleuca                          3.6261707 0.406
Eucalyptus                         1.8114276 0.622
Bare                               7.6450415 0.196
Leaf                               1.7876617 0.629
Other                             11.5242102 0.102
Clay                               0.2928669 0.883
Canopy                            15.1809553 0.182

Site treatments on vegetation

Spinifex

             Df  Sum Sq Mean Sq F value  Pr(>F)  
 TreatCode    4  9.3370  2.3342  3.5866 0.01918 *
 Residuals   25 16.2704  0.6508                  

Using Conn + Setting:

 Conn         1  0.0500  0.0500  0.0666 0.79834  
 Setting      1  5.2734  5.2734  7.0195 0.01331 *
 Residuals   27 20.2840  0.7513                  

Melaleuca

 TreatCode    4  9.1362  2.2840  2.4184 0.07521 .
 Residuals   25 23.6112  0.9444                  

Using Conn + Setting:

 Conn         1  0.020   0.020  0.0165 0.8987
 Setting      1  0.005   0.005  0.0042 0.9487
 Residuals   27 32.722   1.212               

Eucalyptus

 TreatCode    4  38.041   9.510  1.4681 0.2417
 Residuals   25 161.947   6.478               

Using Conn + Setting:

 Conn         1   2.993   2.993  0.4102 0.5273
 Setting      1   0.023   0.023  0.0032 0.9552
 Residuals   27 196.973   7.295               

Bare

 TreatCode    4 51.596  12.899  3.7419 0.01612 *
 Residuals   25 86.181   3.447                  

Using Conn + Setting:

 Conn         1   8.243   8.243  1.7896 0.1921
 Setting      1   5.180   5.180  1.1247 0.2983
 Residuals   27 124.354   4.606               

Leaf

 TreatCode    4 48.475  12.119  3.3267 0.02576 *
 Residuals   25 91.072   3.643                  

Using Conn + Setting:

 Conn         1   3.153   3.153   0.636 0.4321
 Setting      1   2.568   2.568   0.518 0.4779
 Residuals   27 133.827   4.957               

Other

 TreatCode    4  3.2728  0.8182  1.6165 0.2013
 Residuals   25 12.6542  0.5062               

Using Conn + Setting:

 Conn         1  0.6092  0.6092  1.1097 0.3015
 Setting      1  0.4959  0.4959  0.9034 0.3503
 Residuals   27 14.8219  0.5490               

Clay

 TreatCode    4 0.86667 0.21667  2.4074 0.07621 .
 Residuals   25 2.25000 0.09000                  

Using Conn + Setting:

 Conn         1 0.00208 0.00208  0.0181 0.8939
 Setting      1 0.01042 0.01042  0.0906 0.7657
 Residuals   27 3.10417 0.11497               

Canopy

 TreatCode    4 29.880   7.470  2.3542 0.0813 .
 Residuals   25 79.325   3.173                 

Using Conn + Setting:

 Conn         1   0.039   0.039  0.0102 0.9203
 Setting      1   7.315   7.315  1.9392 0.1751
 Residuals   27 101.851   3.772               

LME tests

Spinifex

(this is the simplest model)

                   numDF denDF   F-value p-value
 (Intercept)           1    16 17.531020  0.0007
 Site                  1     4  0.159401  0.7101
 Setting               1    16  9.432623  0.0073 **
 Dune                  1    16  0.305526  0.5881
 Conn                  1    16  1.789425  0.1997
 Site:Setting          1    16  0.257573  0.6187
 Site:Dune             1    16  3.565201  0.0773 .
 Site:Conn             1    16  2.415924  0.1397
 Setting:Dune          1    16  6.875744  0.0185 *
 Site:Setting:Dune     1    16  3.311502  0.0876 .

Melaleuca

                   numDF denDF   F-value p-value
 (Intercept)           1    16 23.785725  0.0002
 Site                  1     4  0.188107  0.6869
 Setting               1    16  0.000052  0.9943
 Dune                  1    16  0.062714  0.8054
 Conn                  1    16  0.004043  0.9501
 Site:Setting          1    16  0.643529  0.4342
 Site:Dune             1    16  0.008394  0.9281
 Site:Conn             1    16  0.683297  0.4206
 Setting:Dune          1    16  8.522505  0.0100 *
 Site:Setting:Dune     1    16  0.674651  0.4235

Eucalyptus

                   numDF denDF   F-value p-value
 (Intercept)           1    16 28.489203  0.0001
 Site                  1     4  1.247650  0.3266
 Setting               1    16  0.054100  0.8190
 Dune                  1    16  2.489434  0.1342
 Conn                  1    16  0.007047  0.9341
 Site:Setting          1    16  5.018700  0.0396 *
 Site:Dune             1    16  0.925821  0.3503
 Site:Conn             1    16  0.001568  0.9689
 Setting:Dune          1    16  3.862923  0.0670
 Site:Setting:Dune     1    16  0.109604  0.7449

Bare

                   numDF denDF  F-value p-value
 (Intercept)           1    16 95.20917  <.0001
 Site                  1     4  0.08328  0.7872
 Setting               1    16  4.28296  0.0550 .
 Dune                  1    16 16.38421  0.0009 ***
 Conn                  1    16  0.23899  0.6316
 Site:Setting          1    16  2.17917  0.1593
 Site:Dune             1    16  0.82198  0.3781
 Site:Conn             1    16  0.57622  0.4588
 Setting:Dune          1    16  0.01863  0.8931
 Site:Setting:Dune     1    16  0.10143  0.7542

Leaf

                   numDF denDF   F-value p-value
 (Intercept)           1    16 179.04456  <.0001
 Site                  1     4   0.18962  0.6857
 Setting               1    16   0.20546  0.6564
 Dune                  1    16  10.11734  0.0058 **
 Conn                  1    16   0.04448  0.8356
 Site:Setting          1    16   3.42148  0.0829 ,
 Site:Dune             1    16   0.00073  0.9787
 Site:Conn             1    16   0.20058  0.6603
 Setting:Dune          1    16   7.92401  0.0125 *
 Site:Setting:Dune     1    16  10.18328  0.0057 **

Other

                   numDF denDF   F-value p-value
 (Intercept)           1    16  8.127317  0.0116
 Site                  1     4  0.174053  0.6980
 Setting               1    16  4.036383  0.0617 .
 Dune                  1    16  2.750591  0.1167
 Conn                  1    16  2.677369  0.1213
 Site:Setting          1    16 11.108120  0.0042 **
 Site:Dune             1    16  4.490934  0.0501 .
 Site:Conn             1    16  0.257868  0.6185
 Setting:Dune          1    16  4.824904  0.0431 *
 Site:Setting:Dune     1    16 12.083409  0.0031 **

Clay

                   numDF denDF   F-value p-value
 (Intercept)           1    16 10.521739  0.0051
 Site                  1     4  1.391304  0.3035
 Setting               1    16  0.057971  0.8128
 Dune                  1    16  8.115942  0.0116 *
 Conn                  1    16  0.760870  0.3960
 Site:Setting          1    16  0.057971  0.8128
 Site:Dune             1    16  0.041408  0.8413
 Site:Conn             1    16  1.552795  0.2307
 Setting:Dune          1    16  0.108696  0.7459
 Site:Setting:Dune     1    16  0.434783  0.5190

Canopy

                   numDF denDF  F-value p-value
 (Intercept)           1    16 60.24224  <.0001
 Site                  1     4  0.01210  0.9177
 Setting               1    16  2.46862  0.1357
 Dune                  1    16  9.51481  0.0071 **
 Conn                  1    16  0.12082  0.7327
 Site:Setting          1    16  5.87667  0.0276 *
 Site:Dune             1    16  0.06077  0.8084
 Site:Conn             1    16  0.00032  0.9860
 Setting:Dune          1    16  0.82124  0.3783
 Site:Setting:Dune     1    16  0.13631  0.7168

NumSpec

                   numDF denDF   F-value p-value
 (Intercept)           1    16 214.26613  <.0001
 Site                  1     4   0.00806  0.9328
 Setting               1    16  10.97852  0.0044 **
 Dune                  1    16   0.02475  0.8770
 Conn                  1    16   0.48114  0.4979
 Site:Setting          1    16   1.50936  0.2370
 Site:Dune             1    16   0.00891  0.9260
 Site:Conn             1    16   6.08257  0.0253 *
 Setting:Dune          1    16   0.37422  0.5493
 Site:Setting:Dune     1    16   0.16632  0.6888

Sum

                   numDF denDF   F-value p-value
 (Intercept)           1    16 149.31845  <.0001
 Site                  1     4   0.70851  0.4473
 Setting               1    16   9.34625  0.0075 **
 Dune                  1    16   0.61018  0.4461
 Conn                  1    16   0.00376  0.9519
 Site:Setting          1    16   0.85425  0.3691
 Site:Dune             1    16   0.17692  0.6796
 Site:Conn             1    16   3.25084  0.0903 .
 Setting:Dune          1    16   0.02633  0.8731
 Site:Setting:Dune     1    16   0.02633  0.8731

LME - log+1 transformed, reptiles

Ctenophorus.fordi

                   numDF denDF   F-value p-value
 (Intercept)           1    16  7.772721  0.0132
 Site                  1     4  0.744309  0.4369
 Setting               1    16 22.816299  0.0002 ***
 Dune                  1    16  2.366991  0.1435
 Conn                  1    16  0.394499  0.5388
 Site:Setting          1    16  2.184868  0.1588
 Site:Dune             1    16  2.366991  0.1435
 Site:Conn             1    16  0.394499  0.5388
 Setting:Dune          1    16  2.761490  0.1160
 Site:Setting:Dune     1    16  2.761490  0.1160

Ctenotus.atlas

                   numDF denDF   F-value p-value
 (Intercept)           1    16 18.289788  0.0006
 Site                  1     4  1.520751  0.2850
 Setting               1    16 12.816642  0.0025 **
 Dune                  1    16  0.008929  0.9259
 Conn                  1    16  0.053576  0.8199
 Site:Setting          1    16  2.812719  0.1129
 Site:Dune             1    16  0.080363  0.7804
 Site:Conn             1    16  0.857210  0.3683
 Setting:Dune          1    16  3.375263  0.0848 .
 Site:Setting:Dune     1    16  0.000000  1.0000

Ctenotus.schomburgkii

                   numDF denDF   F-value p-value
 (Intercept)           1    16  4.670527  0.0462
 Site                  1     4  0.401480  0.5607
 Setting               1    16 11.801718  0.0034 **
 Dune                  1    16  0.128966  0.7242
 Conn                  1    16  0.021494  0.8853
 Site:Setting          1    16  1.014480  0.3288
 Site:Dune             1    16  0.724629  0.4072
 Site:Conn             1    16  0.120771  0.7327
 Setting:Dune          1    16  0.150460  0.7032
 Site:Setting:Dune     1    16  0.845400  0.3715

Lerista.distinguenda

                   numDF denDF   F-value p-value
 (Intercept)           1    16 14.291730  0.0016
 Site                  1     4  0.584284  0.4872
 Setting               1    16 17.280960  0.0007 **
 Dune                  1    16  0.029640  0.8655
 Conn                  1    16  0.282932  0.6021
 Site:Setting          1    16  2.397280  0.1411
 Site:Dune             1    16  0.000009  0.9976
 Site:Conn             1    16  2.457458  0.1365
 Setting:Dune          1    16  0.001735  0.9673
 Site:Setting:Dune     1    16  0.256437  0.6195

Lerista.edwardsae

                   numDF denDF   F-value p-value
 (Intercept)           1    16 26.517125  0.0001
 Site                  1     4  6.378467  0.0650 .
 Setting               1    16  2.765171  0.1158
 Dune                  1    16  1.282132  0.2742
 Conn                  1    16  0.726683  0.4065
 Site:Setting          1    16  4.252312  0.0558 .
 Site:Dune             1    16  2.736159  0.1176
 Site:Conn             1    16  0.181254  0.6760
 Setting:Dune          1    16  1.878315  0.1894
 Site:Setting:Dune     1    16  0.195750  0.6641

Menetia.greyii

                   numDF denDF   F-value p-value
 (Intercept)           1    16 20.488664  0.0003
 Site                  1     4  3.601449  0.1306
 Setting               1    16  6.023564  0.0259 *
 Dune                  1    16  8.690677  0.0094 **
 Conn                  1    16  3.077228  0.0985 .
 Site:Setting          1    16  0.094850  0.7621
 Site:Dune             1    16  5.034130  0.0394 *
 Site:Conn             1    16  0.014135  0.9068
 Setting:Dune          1    16  4.130300  0.0591 .
 Site:Setting:Dune     1    16  0.451971  0.5110

Nephrurus.stellatus

                   numDF denDF  F-value p-value
 (Intercept)           1    16 40.59259  <.0001
 Site                  1     4  0.18498  0.6893
 Setting               1    16  1.62388  0.2207
 Dune                  1    16 11.43736  0.0038 **
 Conn                  1    16  0.92919  0.3494
 Site:Setting          1    16  0.26590  0.6131
 Site:Dune             1    16  0.00549  0.9419
 Site:Conn             1    16  1.01259  0.3293
 Setting:Dune          1    16  0.02695  0.8716
 Site:Setting:Dune     1    16  0.00064  0.9801

Pogona.sp

                   numDF denDF  F-value p-value
 (Intercept)           1    16 8.128058  0.0116
 Site                  1     4 1.180501  0.3383
 Setting               1    16 0.673725  0.4238
 Dune                  1    16 0.105763  0.7492
 Conn                  1    16 0.004713  0.9461
 Site:Setting          1    16 0.148068  0.7055
 Site:Dune             1    16 0.481232  0.4978
 Site:Conn             1    16 0.943386  0.3459
 Setting:Dune          1    16 1.892551  0.1879
 Site:Setting:Dune     1    16 0.075702  0.7867

NumSpec

                   numDF denDF  F-value p-value
 (Intercept)           1    16 594.6073  <.0001
 Site                  1     4   0.1203  0.7462
 Setting               1    16   9.7247  0.0066 **
 Dune                  1    16   0.0595  0.8103
 Conn                  1    16   0.0855  0.7738
 Site:Setting          1    16   1.6931  0.2116
 Site:Dune             1    16   0.0052  0.9436
 Site:Conn             1    16   6.4133  0.0222 *
 Setting:Dune          1    16   0.5176  0.4822
 Site:Setting:Dune     1    16   0.0048  0.9459

Sum

                   numDF denDF  F-value p-value
 (Intercept)           1    16 590.3910  <.0001
 Site                  1     4   1.4137  0.3002
 Setting               1    16   8.0847  0.0117 *
 Dune                  1    16   0.3693  0.5519
 Conn                  1    16   0.2642  0.6143
 Site:Setting          1    16   1.1607  0.2973
 Site:Dune             1    16   0.3376  0.5693
 Site:Conn             1    16   2.7901  0.1143
 Setting:Dune          1    16   0.1216  0.7318
 Site:Setting:Dune     1    16   0.4175  0.5274

Condition

Simplified model

 mod9<-lme(Condition ~  Setting, random = ~1|Block, data=epdata,  method="ML")

             numDF denDF   F-value p-value
 (Intercept)     1    23 234.44723  <.0001
 Setting         1    23  36.29065  <.0001 ***

Notes culled from paper

 The conservation park setting was also significant, as C. fordi was not found in farmland (24%, P = 0.002).

Nephrurus stellatus aspect (26%, P = 0.017) more in dunes

Ctenotus atlas populations were explained by setting (25%, P = 0.012) and condition (23%, P = 0.019). More in cons parks Only appeared in sites with good condition

Lerista distinguenda setting (31%, P = 0.011) more in park Condition (35%, P = 0.001) more in better condition

Lerista edwardsae? Condition (35%, P = 0.003) more in worse sites

Condition

Menetia greyii condition (15%, P = 0.040) - more in worse condition

NumSpec Setting (19%, P = 0.006) more in park Condition (22%, P = 0.002) more in better condition

Sum Setting (28%, P = 0.018) more in park Condition (34%, P = 0.005) more in better

RareSp nothing